alexyermanos / Platypus

R package for the analysis of single-cell immune repertoires
GNU General Public License v3.0
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Loading GEX failed from 'VDJ_GEX_matrix' function #42

Closed LBH2021 closed 1 year ago

LBH2021 commented 1 year ago

I recently tried integrating VDJ and GEX data using the 'VDJ_GEX_matrix' function and the GEX data failed to load (the VDJ data loaded successfully). I previously performed the integration on a subset of my samples using the same file paths and it worked appropriately and the files have not moved. I haven't been able able to figure out where the error is and would appreciate any help you can provide. I have included relevant screenshots below:

Here are the file paths:

Screen Shot 2023-02-27 at 9 20 10 PM

Here is the VDJ_GEX_matrix function:

Screen Shot 2023-02-27 at 9 20 52 PM

Here is the resulting error message:

Screen Shot 2023-02-27 at 9 21 52 PM

Here is the contents of the Cell Ranger 'outs' folder for one of the samples:

Screen Shot 2023-02-27 at 9 51 05 PM

Thank you for your help!

LBH2021 commented 1 year ago

I figured out the error and am closing the issue.